VOSviewer
NVivo
QualCoder
MAXQDA
ATLAS.ti
SciMAT
Taguette
RQDA
Cytoscape
Gephi
Graphviz
KeyLines
UCINET
NodeXL
SocNetV
Pajek
VOSviewer CytoscapeBased on our record, Cytoscape seems to be more popular. It has been mentiond 11 times since March 2021. We are tracking product recommendations and mentions on various public social media platforms and blogs. They can help you identify which product is more popular and what people think of it.
Doing a bit more digging, it's using cytoscape[0] which is similar to graphviz. If you search your favorite search engine with "Cytoscape Session Viewer", you'll find many websites displaying the same type of graphs (select layout: circle). FYI, circo doesn't always output a circle. I recently created https://github.com/MegaManSec/SSH-Snake/blob/main/tools/SSH-Snake-dot-circo.png. - Source: Hacker News / 5 months ago
The YAML files are then parsed, and a CYJS file produced, which is a graph model. This is used directly in the web app, but can also be opened in the Cytoscape desktop app , and imported into Neo4j if desired. I can add additional "export" steps to the automated build process, so e.g. GraphML (yEd, Gephi) or DOT files (GraphViz, mermaid, etc) can be used for whatever purpose needed. Source: 12 months ago
Both Cytoscape and Gephi are options that you can try on Windows; both can run some classic community detection algorithms and can be extended with plugins. Personally, I'd recommend you to use igraph, which can be run as an R or python libraries. Then, about the specific algorithm, I have no experience on amino acid communities, but I would approach the issue thinking the properties that you would like to... Source: over 1 year ago
Two common GUI tools for analysis and editing of graph data are Gephi and Cytoscape. An older alternative starting with a P is Pajek, but I've never used it. Source: almost 2 years ago
I've been thinking that Gephi is getting long in the tooth. Has anybody tried Cytoscape? (https://cytoscape.org/) (DNS is SERVFAILing at the moment.) I use it for a combination of "no K" clustering (general exploration) and what's referred to in threat intelligence by the term of art "pivoting". - Source: Hacker News / about 2 years ago
NVivo - Buy NVivo now for flexible solutions to meet your specific research and data analysis needs.
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
QualCoder - A very complete Free and Open Source Software (FOSS) Computer-Assisted Qualitative Data Analysis Software (CAQDAS) written in Python. It works with text, images, and multimedia such as audios and videos.
Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.
MAXQDA - a professional software for qualitative and mixed methods data analysis
KeyLines - The JavaScript toolkit for graph visualization
